Question: Selecting TCGA samples by barcode in CG Hub
0
gravatar for Max
4.0 years ago by
Max130
Max130 wrote:

I have a list of about 40 barcodes corresponding to TCGA whole exome samples. The CG Hub browser allows one to search by sample type, platform, assembly, library, etc. but not by barcode. If I restrict by the existing filters, I have about 650 samples that I still need to go through by hand to find the 40 or so that I need. Surely there must be a way to search and download specific TCGA barcodes from a list in CG Hub. Does anybody know how to do this?

cghub tcga • 1.6k views
ADD COMMENTlink modified 4.0 years ago by Cyriac Kandoth5.3k • written 4.0 years ago by Max130
3
gravatar for Cyriac Kandoth
4.0 years ago by
Cyriac Kandoth5.3k
Memorial Sloan Kettering, New York, USA
Cyriac Kandoth5.3k wrote:

The barcodes are metadata. You can use the little box on the top-right to search for specific barcodes. Or you can build HTTP queries like this:

https://browser.cghub.ucsc.edu/search/?state=(live)&q=TCGA-AB-2807

If you want to do this more automatically with some scripts that query each of your 40 barcodes, then I'd recommend using the cgquery command-line tool available here

Update (Nov 2016): CGHub has shut down, and a lot of TCGA's original data portal infrastructure. All sequence data has been harmonized to GRCh38 and is hosted out of NCI's GDC Portal. If you want the original legacy data based in GRCh37, use this link.

ADD COMMENTlink modified 2.4 years ago • written 4.0 years ago by Cyriac Kandoth5.3k

Thank you, I think that using cgquery may be our best option.

ADD REPLYlink written 4.0 years ago by Max130
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